1883, sixteenth year of the Meiji age, Tokei (Tokyo). Shizume Kurahashi, a "worshipper" of the scientific method, suffers of a particular disturb: when her heartbeats become irregular she falls in a sleep full of nightmares, while an arachnid-like creature appears from her chest. Can this be explained with scientific reasons? Shizume believes that the answer is yes and she will do anything for demonstrating it... although his father, the divinator Hikofumi Kurahashi, misteriously disappeared and the intrepid secret agent Kogenta Inui is searching him in a unsure Lovecraftian context.

Strange events happen around the capital city of a country that is beginning to get closer to the Western world, and science, superstition, misterious diseases and hidden sects start to be tied by a unique common denominator that every people call "Tsukumo".